yep, themes may use colors but user will set them by himself so where is trouble? by default this option may be set to off(all 3 of them) and with activation i think user ought to understand what he's doing so capable to set colors with no conflict to his theme.
or if you want to present this feature to wide number of users with less trouble(so option turned on by default), just set styles and set no color, but at least give geek-users an ability to change all these to their liking.
or if you want to present this feature to wide number of users with less trouble(so option turned on by default), just set styles and set no color, but at least give geek-users an ability to change all these to their liking.